Rules or Checklist? Which would you prefer from the OBO Foundry?

[Update: Duncan’s written a call for comments on the OBO Foundry criteria on his blog. Also posting on this are Melanie and Frank. Take a look! Update 2: I should have called the 10 criteria “principles” rather than “rules”. My apologies. I think the title may be a little bit of a misnomer for the post. I’m not sure you need to choose between principles and checklists. It’s nice to have the “short and sweet” and the detailed.]

The OBO FoundryWorkshop (OBO Foundry paper) is coming up this weekend, and Duncan Hull and I were talking about the 10 criteria the Foundry has for member ontologies. We had been wondering what sort of questions we would ask the OBO Foundry people if we wanted to see the 10 criteria “upgraded” to a minimal checklist for OBO Foundry ontologies in the style of MIBBI. As a result of that, here are my thoughts on each criterion. Perhaps some of these have been answered in mailing lists or elsewhere, but they’re not visible on the OBO Foundry site. Hopefully this post would be useful as a starting point for a discussion on more complete definitions and explanations for the minimal requirements of an OBO Foundry ontology.

Each criterion is reproduced in bold, with my opinions after in italicised text. For any further text present in the criteria list, please see the list page itself.

The ontology must be open and available to be used by all without any constraint other than (a) its origin must be acknowledged and (b) it is not to be altered and subsequently redistributed under the original name or with the same identifiers.This is a license without a name or a strong structure. Is it a first attempt at an OBO-specific license? If so, it is too generic to be of much use. Alternatively, is it a requirements list for choosing an existing license? Or, as another option, are they suggesting that people choose their own licenses along these lines? I believe strongly that already-extant licenses should be used in biological research wherever possible. You can see a summary of a FriendFeed discussion and an email discussion with Science Commons in my blog post on Choosing a License for Your Ontology for my opinion on the subject. Therefore I would suggest option 2, with the Foundry choosing an appropriate license (or shortlist of compatible licenses) as soon as they could.

The ontology is in, or can be expressed in, a common shared syntax. This may be either the OBO syntax, extensions of this syntax, or OWL.
Firstly, I would like clarification of what “extensions of the [OBO] syntax” means. Secondly, just saying “OWL” as a syntax is too vague; there’s OWL-Full, OWL-DL, and OWL-Lite, to name a few. Are all acceptable, or is the most commonly-used (OWL-DL) the one they want people to use?

The ontologies possesses a unique identifier space within the OBO Foundry.Aside from the (nitpicky) statement that it should be either “The ontologies possess” or “Each ontology possesses”, this is one of the most useful criteria. However, a little more detail would be useful here. What should come after the prefix? An underscore or some other dividing character? The rest of the identifier without a dividing character? Should the OBO Foundry assign a prefix to avoid confusion? By the way, a paper has just been published about the *naming* conventions for the OBO Foundry which is interesting. This isn’t the same thing as this criterion, which is about unique identifiers, but it’s still worth a read.

The ontology provider has procedures for identifying distinct successive versions.A little vague, but that probably cannot be helped, as you probably don’t want to legislate the type of versioning that takes place with each ontology. Links out to GO’s procedures or OBI’s procedures might provide some ideas to people who don’t know what versioning to use.

The ontology has a clearly specified and clearly delineated content.The “domain” of the ontology, used in the further description of this criterion, is a vague term. Yes, we all want orthogonality, but that is difficult to achieve in practice and a clearer description of how people can achieve it might be useful. How are two terms expressing the same concept in the different ontologies resolved? Via the mailing list? Is there an established procedure? It’s easy to say that no two terms should be covering the same concept, but harder to check. There’s been some recent papers in finding similar concepts within a single ontology (e.g. 10.1093/bioinformatics/btp195) might be applicable to multiple ontologies.

The ontologies include textual definitions for all terms.Good point. It would also be nice to say formal logic statements for classes would be useful (but not required), as it might help ensure the internal consistency of Foundry ontologies.

The ontology uses relations which are unambiguously defined following the pattern of definitions laid down in the OBO Relation Ontology.
This says you have to define your relations “following the pattern” from the RO. Does this mean all your relations must be children of relations in RO, or just that you follow their style? Probably the latter, but this is unclear at the moment.

The ontology is well documented.
Definitely! But how? Where? In the ontology file? On a website? Does the OBO website provide the ability to have lots of documentation, or should it just be links out?

The ontology has a plurality of independent users.
I’m a bit of a failure here, as I don’t know what this means. I can think of at least 2-3 different ways of interpreting this. What are users in this context? What makes them independent? How can you tell what your users are?

The ontology will be developed collaboratively with other OBO Foundry members.
Great idea. But what if you can’t find anyone who wants to help? Does that mean you can’t develop? Again, perhaps this just means regular reviews of the developing ontology by other OBO members, but could be made clearer.

Most of these opinions don’t try to provide an answer, but instead just raise some questions that the attendees at this week’s workshop might like to have in their minds. If the OBO Foundry, which exists to “align ontology development efforts” doesn’t provide clear guidance, there is a risk that each member ontology would come up with their own answers, thus negating some of the benefits provided by their membership (quote from the Nature Biotech paper).